Occasionally when Bamboo is doing a clone of a new repository the folder in _hg-repositories-cache is created and it looks like it attempts to check out the repository but no .hg file or folder is created.
I don't remember the exact issue number, but I remember there was a problem on Windows when antivirus software was enabled on that directory. Try excluding that directory and see if it helps.
You may try upgrading to a later Bamboo version, it should contain a more graceful handling of that case.
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